Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line

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Wahl MB, Caldwell RB, Kierzek AM, Arakawa H, Eyras E, Hubner N, Jung C, Soeldenwagner M, Cervelli M, Wang YD, Liebscher V, Buerstedde JM. Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line. BMC Genomics. 2004; 5: 98. DOI: 10.1186/1471-2164-5-98
http://hdl.handle.net/10230/16422
To cite or link this document: http://hdl.handle.net/10230/16422
dc.contributor.author Wahl, Matthias B.
dc.contributor.author Caldwell, Randolph B.
dc.contributor.author Kierzek, Andrzej M.
dc.contributor.author Arakawa, Hirosi
dc.contributor.author Eyras Jiménez, Eduardo
dc.contributor.author Hubner, Nina
dc.contributor.author Jung, Christian
dc.contributor.author Soeldenwagner, Manuel
dc.contributor.author Cervelli, Manuela
dc.contributor.author Wang, Yan-Dong
dc.contributor.author Liebscher, Volkmar
dc.contributor.author Buerstedde, Jean-Marie
dc.date.accessioned 2012-05-09T07:32:18Z
dc.date.available 2012-05-09T07:32:18Z
dc.date.issued 2004
dc.identifier.citation Wahl MB, Caldwell RB, Kierzek AM, Arakawa H, Eyras E, Hubner N, Jung C, Soeldenwagner M, Cervelli M, Wang YD, Liebscher V, Buerstedde JM. Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line. BMC Genomics. 2004; 5: 98. DOI: 10.1186/1471-2164-5-98
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10230/16422
dc.description.abstract Background: The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures, translated open reading frames (ORFs) and flanking untranslated regions. The best currently available chicken transcript catalog is the Ensembl build based on the mappings of a relatively small number of full length cDNAs and ESTs to the genome as well as genome sequence derived in silico gene predictions. Results: We use Long Serial Analysis of Gene Expression (LongSAGE) in bursal lymphocytes and the DT40 cell line to verify the quality and completeness of the annotated transcripts. 53.6% of the more than 38,000 unique SAGE tags (unitags) match to full length bursal cDNAs, the Ensembl transcript build or the genome sequence. The majority of all matching unitags show single matches to the genome, but no matches to the genome derived Ensembl transcript build. Nevertheless, most of these tags map close to the 3' boundaries of annotated Ensembl transcripts. Conclusions: These results suggests that rather few genes are missing in the current Ensembl chicken transcript build, but that the 3' ends of many transcripts may not have been accurately predicted. The tags with no match in the transcript sequences can now be used to improve gene predictions, pinpoint the genomic location of entirely missed transcripts and optimize the accuracy of gene finder software.
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof BMC Genomics. 2004; 5: 98
dc.rights (c) 2004 Wahl et al. Creative Commons Attribution License
dc.rights.uri http://creativecommons.org/licenses/by/2.0/
dc.subject.other Cèl·lules eucariotes -- Aspectes genètics
dc.subject.other Expressió genètica
dc.title Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/1471-2164-5-98
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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